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Owing to efficient proteolysis and particular advantages of trypsin-generated peptides, trypsin is the most widely used protease in mass spectrometry. However, it is often overlooked that trypsin has shortcomings such as incomplete proteolysis, poor digestion of tightly folded proteins or an inability to cleave arginine and lysine residues adjacent to proline. These shortcomings negatively affect mass spec analysis, particularly advanced applications such as protein quantitation.

We show here that Lys-C and Arg-C proteases address trypsin shortcomings. By supplementing trypsin with Lys-C we have achieved >95% digestion efficiency as judged by the level of completely digested peptides. In addition, by utilizing the remarkable resistance of Lys-C to denaturing conditions we have adapted this trypsin/Lys-C mix to digest a proteolytically resistant protein. Finally, we demonstrate the unique utility of Arg-C protease based on its ability to cleave the residues adjacent to proline.

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